[2024-01-24 14:54:56,530] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,532] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2386ae0-c6d6-42ea-9097-c60557157248/dqc_reference
[2024-01-24 14:54:57,824] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,825] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,825] [INFO] Running command: gunzip -c /var/lib/cwl/stgec1b93bf-121f-4046-99fb-a1a46e4cd28e/GCF_016902375.1_ASM1690237v1_genomic.fna.gz | prodigal -d GCF_016902375.1_ASM1690237v1_genomic.fna/cds.fna -a GCF_016902375.1_ASM1690237v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:17,697] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:17,698] [INFO] Task started: HMMsearch
[2024-01-24 14:55:17,698] [INFO] Running command: hmmsearch --tblout GCF_016902375.1_ASM1690237v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2386ae0-c6d6-42ea-9097-c60557157248/dqc_reference/reference_markers.hmm GCF_016902375.1_ASM1690237v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:17,991] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:17,992] [INFO] Found 6/6 markers.
[2024-01-24 14:55:18,025] [INFO] Query marker FASTA was written to GCF_016902375.1_ASM1690237v1_genomic.fna/markers.fasta
[2024-01-24 14:55:18,025] [INFO] Task started: Blastn
[2024-01-24 14:55:18,025] [INFO] Running command: blastn -query GCF_016902375.1_ASM1690237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2386ae0-c6d6-42ea-9097-c60557157248/dqc_reference/reference_markers.fasta -out GCF_016902375.1_ASM1690237v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:18,653] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:18,656] [INFO] Selected 24 target genomes.
[2024-01-24 14:55:18,656] [INFO] Target genome list was writen to GCF_016902375.1_ASM1690237v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:18,665] [INFO] Task started: fastANI
[2024-01-24 14:55:18,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgec1b93bf-121f-4046-99fb-a1a46e4cd28e/GCF_016902375.1_ASM1690237v1_genomic.fna.gz --refList GCF_016902375.1_ASM1690237v1_genomic.fna/target_genomes.txt --output GCF_016902375.1_ASM1690237v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:34,364] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:34,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2386ae0-c6d6-42ea-9097-c60557157248/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:34,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2386ae0-c6d6-42ea-9097-c60557157248/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:34,383] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:34,384] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:34,384] [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
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	78.7957	154	1174	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	78.7357	296	1174	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	78.7015	279	1174	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	78.6738	319	1174	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	78.6031	291	1174	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	78.5871	321	1174	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	78.5684	322	1174	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	78.5667	318	1174	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	78.5406	286	1174	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	78.5337	314	1174	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	78.4916	292	1174	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	78.4592	289	1174	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	78.4179	156	1174	95	below_threshold
Bacteroides fragilis	strain=CCUG4856T	GCA_005706655.1	817	817	type	True	78.3632	145	1174	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	78.3226	146	1174	95	below_threshold
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	78.2996	141	1174	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	78.2762	156	1174	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_000025985.1	817	817	type	True	78.2747	146	1174	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	78.2607	145	1174	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	78.1768	151	1174	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	78.1683	154	1174	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	78.1623	151	1174	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	78.1412	234	1174	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_000169015.1	47678	47678	suspected-type	True	78.1107	150	1174	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:34,385] [INFO] DFAST Taxonomy check result was written to GCF_016902375.1_ASM1690237v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:34,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:34,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:34,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2386ae0-c6d6-42ea-9097-c60557157248/dqc_reference/checkm_data
[2024-01-24 14:55:34,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:34,424] [INFO] Task started: CheckM
[2024-01-24 14:55:34,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016902375.1_ASM1690237v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016902375.1_ASM1690237v1_genomic.fna/checkm_input GCF_016902375.1_ASM1690237v1_genomic.fna/checkm_result
[2024-01-24 14:56:31,565] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:31,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:31,588] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:31,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:31,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016902375.1_ASM1690237v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:31,590] [INFO] Task started: Blastn
[2024-01-24 14:56:31,590] [INFO] Running command: blastn -query GCF_016902375.1_ASM1690237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2386ae0-c6d6-42ea-9097-c60557157248/dqc_reference/reference_markers_gtdb.fasta -out GCF_016902375.1_ASM1690237v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:32,509] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:32,513] [INFO] Selected 12 target genomes.
[2024-01-24 14:56:32,513] [INFO] Target genome list was writen to GCF_016902375.1_ASM1690237v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:32,528] [INFO] Task started: fastANI
[2024-01-24 14:56:32,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgec1b93bf-121f-4046-99fb-a1a46e4cd28e/GCF_016902375.1_ASM1690237v1_genomic.fna.gz --refList GCF_016902375.1_ASM1690237v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016902375.1_ASM1690237v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:41,884] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:41,899] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:41,900] [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_900130135.1	s__Bacteroides togonis	97.351	957	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	conclusive
GCA_019116805.1	s__Bacteroides merdavium	87.6038	669	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128475.1	s__Bacteroides massiliensis	86.388	717	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCF_900108345.1	s__Bacteroides ndongoniae	81.2708	469	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	-
GCA_900553815.1	s__Bacteroides sp900553815	80.4418	331	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.95	97.95	0.73	0.73	2	-
GCA_905201685.1	s__Bacteroides sp905201685	79.9456	204	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883785.1	s__Bacteroides intestinipullorum	78.9749	245	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374365.1	s__Bacteroides gallinarum	78.6025	291	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000154205.1	s__Bacteroides uniformis	78.5478	320	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCA_017471925.1	s__Bacteroides sp017471925	78.5399	266	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154525.1	s__Bacteroides stercoris	78.4776	295	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_002160055.1	s__Bacteroides avicola	78.4291	269	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.46	98.46	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:41,902] [INFO] GTDB search result was written to GCF_016902375.1_ASM1690237v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:41,902] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:41,906] [INFO] DFAST_QC result json was written to GCF_016902375.1_ASM1690237v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:41,907] [INFO] DFAST_QC completed!
[2024-01-24 14:56:41,907] [INFO] Total running time: 0h1m45s