[2024-01-24 12:31:57,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:57,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:57,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg452674c0-16dc-46f2-bc71-d2edd1fdcc98/dqc_reference
[2024-01-24 12:31:58,572] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:58,573] [INFO] Task started: Prodigal
[2024-01-24 12:31:58,573] [INFO] Running command: gunzip -c /var/lib/cwl/stg96f7d6bd-17fb-45d0-9507-9598a19cde31/GCF_022662015.1_ASM2266201v1_genomic.fna.gz | prodigal -d GCF_022662015.1_ASM2266201v1_genomic.fna/cds.fna -a GCF_022662015.1_ASM2266201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:14,400] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:14,400] [INFO] Task started: HMMsearch
[2024-01-24 12:32:14,401] [INFO] Running command: hmmsearch --tblout GCF_022662015.1_ASM2266201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg452674c0-16dc-46f2-bc71-d2edd1fdcc98/dqc_reference/reference_markers.hmm GCF_022662015.1_ASM2266201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:14,710] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:14,711] [INFO] Found 6/6 markers.
[2024-01-24 12:32:14,751] [INFO] Query marker FASTA was written to GCF_022662015.1_ASM2266201v1_genomic.fna/markers.fasta
[2024-01-24 12:32:14,752] [INFO] Task started: Blastn
[2024-01-24 12:32:14,752] [INFO] Running command: blastn -query GCF_022662015.1_ASM2266201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg452674c0-16dc-46f2-bc71-d2edd1fdcc98/dqc_reference/reference_markers.fasta -out GCF_022662015.1_ASM2266201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:15,408] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:15,412] [INFO] Selected 17 target genomes.
[2024-01-24 12:32:15,412] [INFO] Target genome list was writen to GCF_022662015.1_ASM2266201v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:15,419] [INFO] Task started: fastANI
[2024-01-24 12:32:15,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg96f7d6bd-17fb-45d0-9507-9598a19cde31/GCF_022662015.1_ASM2266201v1_genomic.fna.gz --refList GCF_022662015.1_ASM2266201v1_genomic.fna/target_genomes.txt --output GCF_022662015.1_ASM2266201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:25,870] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:25,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg452674c0-16dc-46f2-bc71-d2edd1fdcc98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:25,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg452674c0-16dc-46f2-bc71-d2edd1fdcc98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:25,885] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:25,885] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:25,885] [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
Aestuariivivens sediminicola	strain=MTV5-3	GCA_022662015.1	2913560	2913560	type	True	100.0	1205	1206	95	conclusive
Aestuariivivens sediminis	strain=S-DT1-15	GCA_022662105.1	2913557	2913557	type	True	79.4733	527	1206	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	78.2849	301	1206	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.8104	299	1206	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	77.5363	198	1206	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.4946	130	1206	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.4832	125	1206	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.4513	123	1206	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.3295	101	1206	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.1469	115	1206	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.9369	73	1206	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.8405	149	1206	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.829	149	1206	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	76.7298	165	1206	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.7018	100	1206	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	76.6842	140	1206	95	below_threshold
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	76.5692	71	1206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:25,891] [INFO] DFAST Taxonomy check result was written to GCF_022662015.1_ASM2266201v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:25,892] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:25,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:25,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg452674c0-16dc-46f2-bc71-d2edd1fdcc98/dqc_reference/checkm_data
[2024-01-24 12:32:25,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:25,934] [INFO] Task started: CheckM
[2024-01-24 12:32:25,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022662015.1_ASM2266201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022662015.1_ASM2266201v1_genomic.fna/checkm_input GCF_022662015.1_ASM2266201v1_genomic.fna/checkm_result
[2024-01-24 12:33:13,530] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:13,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:13,556] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:13,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:13,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022662015.1_ASM2266201v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:13,558] [INFO] Task started: Blastn
[2024-01-24 12:33:13,558] [INFO] Running command: blastn -query GCF_022662015.1_ASM2266201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg452674c0-16dc-46f2-bc71-d2edd1fdcc98/dqc_reference/reference_markers_gtdb.fasta -out GCF_022662015.1_ASM2266201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:14,406] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:14,412] [INFO] Selected 32 target genomes.
[2024-01-24 12:33:14,412] [INFO] Target genome list was writen to GCF_022662015.1_ASM2266201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:14,462] [INFO] Task started: fastANI
[2024-01-24 12:33:14,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg96f7d6bd-17fb-45d0-9507-9598a19cde31/GCF_022662015.1_ASM2266201v1_genomic.fna.gz --refList GCF_022662015.1_ASM2266201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022662015.1_ASM2266201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:32,230] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:32,258] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:33:32,258] [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_900115185.1	s__Algorimicrobium echini	77.5598	85	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	-
GCF_006148925.1	s__Algibacter_D aestuarii	77.5363	198	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	77.5077	167	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358095.2	s__Seonamhaeicola sp004358095	77.4975	161	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.4946	130	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	77.4832	125	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016827605.1	s__Jejuia sp016827605	77.4513	123	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002895005.1	s__Hanstruepera neustonica	77.3295	101	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hanstruepera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826645.1	s__Psychroserpens mesophilus	77.3286	92	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202195.1	s__Oceanihabitans iliipiscarium	77.327	85	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006974145.1	s__Changchengzhania lutea	77.2061	144	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Changchengzhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910715.1	s__Flavivirga sp012910715	77.162	164	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645385.1	s__Winogradskyella sp015645385	77.1602	69	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014270105.1	s__Jejuia sp014270105	77.1469	115	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.14	140	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	77.1095	141	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	77.067	143	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	77.0083	81	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	76.8584	147	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014596975.1	s__Aestuariibaculum marinum	76.8341	137	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009746565.1	s__Mariniflexile sp002426835	76.7974	107	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	98.94	98.94	0.97	0.97	2	-
GCF_014646655.1	s__Yeosuana aromativorans	76.7332	166	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807055.1	s__Confluentibacter citreus	76.7282	128	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280395.1	s__Confluentibacter sp002280395	76.7045	82	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047595.1	s__CAU-1491 sp005047595	76.7018	100	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843175.1	s__Confluentibacter flavum	76.7002	139	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	76.6959	68	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425645.1	s__Gaetbulibacter saemankumensis	76.6276	143	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gaetbulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997285.1	s__Gelidibacter salicanalis	76.5993	70	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238425.1	s__JABABD01 sp014238425	76.2828	57	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__JABABD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067265.1	s__Oceanihabitans sp018067265	76.2727	60	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222915.1	s__Psychroserpens sp018222915	76.121	86	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:32,260] [INFO] GTDB search result was written to GCF_022662015.1_ASM2266201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:32,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:32,265] [INFO] DFAST_QC result json was written to GCF_022662015.1_ASM2266201v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:32,266] [INFO] DFAST_QC completed!
[2024-01-24 12:33:32,266] [INFO] Total running time: 0h1m35s