[2024-01-24 10:47:40,955] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,956] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,956] [INFO] DQC Reference Directory: /var/lib/cwl/stg929042b4-f8cb-4669-bcc1-602b1291bae1/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgeab353d2-3cd2-4dac-ab80-7bab8a1cfeb8/GCF_019703855.1_ASM1970385v1_genomic.fna.gz | prodigal -d GCF_019703855.1_ASM1970385v1_genomic.fna/cds.fna -a GCF_019703855.1_ASM1970385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:56,204] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:56,205] [INFO] Task started: HMMsearch
[2024-01-24 10:47:56,205] [INFO] Running command: hmmsearch --tblout GCF_019703855.1_ASM1970385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg929042b4-f8cb-4669-bcc1-602b1291bae1/dqc_reference/reference_markers.hmm GCF_019703855.1_ASM1970385v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:56,514] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:56,515] [INFO] Found 6/6 markers.
[2024-01-24 10:47:56,553] [INFO] Query marker FASTA was written to GCF_019703855.1_ASM1970385v1_genomic.fna/markers.fasta
[2024-01-24 10:47:56,553] [INFO] Task started: Blastn
[2024-01-24 10:47:56,553] [INFO] Running command: blastn -query GCF_019703855.1_ASM1970385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg929042b4-f8cb-4669-bcc1-602b1291bae1/dqc_reference/reference_markers.fasta -out GCF_019703855.1_ASM1970385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:57,197] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:57,200] [INFO] Selected 20 target genomes.
[2024-01-24 10:47:57,200] [INFO] Target genome list was writen to GCF_019703855.1_ASM1970385v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:57,229] [INFO] Task started: fastANI
[2024-01-24 10:47:57,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgeab353d2-3cd2-4dac-ab80-7bab8a1cfeb8/GCF_019703855.1_ASM1970385v1_genomic.fna.gz --refList GCF_019703855.1_ASM1970385v1_genomic.fna/target_genomes.txt --output GCF_019703855.1_ASM1970385v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:13,528] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:13,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg929042b4-f8cb-4669-bcc1-602b1291bae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:13,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg929042b4-f8cb-4669-bcc1-602b1291bae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:13,538] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:13,539] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:13,539] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Desulfomarina profundi	strain=KT2	GCA_019703855.1	2772557	2772557	type	True	100.0	1434	1435	95	conclusive
Desulfosediminicola flagellatus	strain=IMCC35005	GCA_005116655.2	2569541	2569541	type	True	77.4906	83	1435	95	below_threshold
Desulforhopalus singaporensis	strain=DSM 12130	GCA_900104445.1	91360	91360	type	True	76.779	78	1435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:13,540] [INFO] DFAST Taxonomy check result was written to GCF_019703855.1_ASM1970385v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:13,541] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:13,541] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:13,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg929042b4-f8cb-4669-bcc1-602b1291bae1/dqc_reference/checkm_data
[2024-01-24 10:48:13,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:13,584] [INFO] Task started: CheckM
[2024-01-24 10:48:13,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019703855.1_ASM1970385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019703855.1_ASM1970385v1_genomic.fna/checkm_input GCF_019703855.1_ASM1970385v1_genomic.fna/checkm_result
[2024-01-24 10:48:51,363] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:51,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:51,388] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:51,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:51,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019703855.1_ASM1970385v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:51,389] [INFO] Task started: Blastn
[2024-01-24 10:48:51,389] [INFO] Running command: blastn -query GCF_019703855.1_ASM1970385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg929042b4-f8cb-4669-bcc1-602b1291bae1/dqc_reference/reference_markers_gtdb.fasta -out GCF_019703855.1_ASM1970385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:52,477] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:52,481] [INFO] Selected 29 target genomes.
[2024-01-24 10:48:52,481] [INFO] Target genome list was writen to GCF_019703855.1_ASM1970385v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:52,503] [INFO] Task started: fastANI
[2024-01-24 10:48:52,503] [INFO] Running command: fastANI --query /var/lib/cwl/stgeab353d2-3cd2-4dac-ab80-7bab8a1cfeb8/GCF_019703855.1_ASM1970385v1_genomic.fna.gz --refList GCF_019703855.1_ASM1970385v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019703855.1_ASM1970385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:08,916] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:08,936] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:49:08,936] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_005116655.2	s__Desulfopila sp005116655	77.7114	84	1435	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001750925.1	s__Desulforhopalus sp001750925	77.1045	119	1435	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	99.42	99.36	0.78	0.73	3	-
GCA_000961725.1	s__Desulforhopalus sp000961725	77.0136	94	1435	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352445.1	s__Desulforhopalus sp002352445	76.9429	147	1435	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015662865.1	s__Desulfocapsa sulfexigens_B	76.725	52	1435	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104445.1	s__Desulforhopalus singaporensis	76.712	77	1435	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116645.1	s__Desulforhopalus sp005116645	76.508	113	1435	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390165.1	s__Desulforhopalus sp011390165	76.2755	54	1435	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018817385.1	s__Desulfocapsa sp018817385	75.9983	56	1435	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfocapsa	95.0	99.94	99.94	0.97	0.97	2	-
GCA_903901335.1	s__CAIUQR01 sp903901335	75.9182	60	1435	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__CAIUQR01	95.0	99.73	99.56	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:08,938] [INFO] GTDB search result was written to GCF_019703855.1_ASM1970385v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:08,939] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:08,943] [INFO] DFAST_QC result json was written to GCF_019703855.1_ASM1970385v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:08,943] [INFO] DFAST_QC completed!
[2024-01-24 10:49:08,943] [INFO] Total running time: 0h1m28s