seqwish std::invalid_argument error about pggb HOT 11 CLOSED

You can't use the wfmash-xxxx file as -a/--input-paf because it is a temporary file of wfmash that contains only the mappings, that is the regions to align, so there are no CIGAR strings in it. seqwish warns you of this ([seqwish] WARNING: input alignment file wfmash-3TaQ4Q does not have CIGAR strings). Moreover, it seems that such a file presents invalid information in it, which is triggering the error. Try running pggb by using the output of wfmash (in your case, it should be called output/wfash-3TaQ4Q.paf).

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@AndreaGuarracino
Thank you for your quickly reply! But when I use pggb -i 19-genomes.merge.fa -n 19 -o output -p 90 -s 100000 -t 5 -T 5 -M -Z to create the pan-genome graph, it cannot generate the paf file. There is only a wfmash-3TaQ4Q temp file.

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Weird, or maybe you haven't waited long enough. What does the estimated mapping and alignment time say in the log? I suggest reducing -s 50000 and waiting a bit more. If the problem persists, please share the output/...log file.

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It occurs the following log at last.

[E::fai_load3_core] Failed to open FASTA file 19-genomes.merge.fa
wfmash -X -s 100000 -p 90 -n 18 -t 16 19-genomes.merge.fa 19-genomes.merge.fa
15440.41s user 792.33s system 1172% cpu 1384.73s total 7245936Kb max memory

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log.txt

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[E::fai_load3_core] Failed to open FASTA file 19-genomes.merge.fa

It is not able to see the FASTA file in input, very strange. Can I see your 19-genomes.merge.fa.fai file too? And also head /home/cuixb/data/analysis_data/graph-pan-genome/pggb-result/wfmash-3TaQ4Q?

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19-genomes.merge.fa.fai file:
19-genomes.merge.fa.zip

head of wfmash-3TaQ4Q file:

Darmor_v10#1#A01	32958928	27800000	28300000	+	Darmor_v10#1#C01	48239358	47247687	47879060	5741	631373	10	id:f:90.9308
Darmor_v10#1#A01	32958928	0	3800000	+	Darmor_v5#1#chrC01	38829317	850	4733913	44055	4733063	12	id:f:93.0793
Darmor_v10#1#A01	32958928	27000000	29700000	+	Darmor_v5#1#chrC01	38829317	35738139	38333401	25321	2700000	12	id:f:93.7809
Darmor_v10#1#A01	32958928	30500000	31200000	+	Darmor_v5#1#chrC01	38829317	38267435	38823342	6814	700000	16	id:f:97.3442
Darmor_v10#1#A01	32958928	29900000	30500000	-	Darmor_v5#1#chrAnn_random	48658326	1918964	2515790	5847	600000	16	id:f:97.4553
Darmor_v10#1#A01	32958928	15700000	16300000	-	Darmor_v5#1#chrAnn_random	48658326	3155785	3717399	5876	600000	17	id:f:97.9259
Darmor_v10#1#A01	32958928	27800000	28300000	+	Express617#1#chrC01	44118044	38888171	39510831	5664	622660	10	id:f:90.972
Darmor_v10#1#A01	32958928	28700000	29900000	+	Express617#1#chrC01	44118044	40944888	42168781	11515	1223893	12	id:f:94.0823
Darmor_v10#1#A01	32958928	27800000	28300000	+	FAFU_ZS11#1#chrC01	54641295	49487432	50101595	5581	614163	10	id:f:90.8653
Darmor_v10#1#A01	32958928	31200000	31900000	+	FAFU_ZS11#1#chrC01	54641295	50286548	50945152	6412	700000	11	id:f:91.6069

the whole wfmash-3TaQ4Q file:
wfmash-3TaQ4Q.zip

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The FASTA index seems healthy. The input contains a lot of sequences, but I don't think (hope) that's the problem. Can you try it with other, but smaller FASTA files? With FASTA files in the same folder where your current input is, and also FASTA files present in other folders? I am wondering if there is an issue that is specific to your system. In each test, please also delete and regenerate the FASTA index, to be safe.

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@ekg As you said, I have confirmed the number of sequences of the reference genome and both two files return the same value.

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When I reinstall the whole environment for pggb using conda, it runs successfully without error.

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