[2023-03-15 23:56:02,649] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:56:02,651] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:56:02,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d63e251-0fd7-4cb6-b0f3-c6f46ab6afdf/dqc_reference
[2023-03-15 23:56:03,748] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:56:03,749] [INFO] Task started: Prodigal
[2023-03-15 23:56:03,749] [INFO] Running command: cat /var/lib/cwl/stg006b4de1-26a0-4af8-ad71-ce9b3b95722b/OceanDNA-b10736.fa | prodigal -d OceanDNA-b10736/cds.fna -a OceanDNA-b10736/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:56:09,986] [INFO] Task succeeded: Prodigal
[2023-03-15 23:56:09,987] [INFO] Task started: HMMsearch
[2023-03-15 23:56:09,987] [INFO] Running command: hmmsearch --tblout OceanDNA-b10736/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d63e251-0fd7-4cb6-b0f3-c6f46ab6afdf/dqc_reference/reference_markers.hmm OceanDNA-b10736/protein.faa > /dev/null
[2023-03-15 23:56:10,152] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:56:10,153] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg006b4de1-26a0-4af8-ad71-ce9b3b95722b/OceanDNA-b10736.fa]
[2023-03-15 23:56:10,180] [INFO] Query marker FASTA was written to OceanDNA-b10736/markers.fasta
[2023-03-15 23:56:10,181] [INFO] Task started: Blastn
[2023-03-15 23:56:10,181] [INFO] Running command: blastn -query OceanDNA-b10736/markers.fasta -db /var/lib/cwl/stg1d63e251-0fd7-4cb6-b0f3-c6f46ab6afdf/dqc_reference/reference_markers.fasta -out OceanDNA-b10736/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:56:10,738] [INFO] Task succeeded: Blastn
[2023-03-15 23:56:10,742] [INFO] Selected 23 target genomes.
[2023-03-15 23:56:10,742] [INFO] Target genome list was writen to OceanDNA-b10736/target_genomes.txt
[2023-03-15 23:56:10,782] [INFO] Task started: fastANI
[2023-03-15 23:56:10,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg006b4de1-26a0-4af8-ad71-ce9b3b95722b/OceanDNA-b10736.fa --refList OceanDNA-b10736/target_genomes.txt --output OceanDNA-b10736/fastani_result.tsv --threads 1
[2023-03-15 23:56:23,685] [INFO] Task succeeded: fastANI
[2023-03-15 23:56:23,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d63e251-0fd7-4cb6-b0f3-c6f46ab6afdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:56:23,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d63e251-0fd7-4cb6-b0f3-c6f46ab6afdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:56:23,697] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:56:23,698] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:56:23,698] [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
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	79.7389	122	203	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	79.7334	127	203	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	78.3599	90	203	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.3476	91	203	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.3465	91	203	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.3438	90	203	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.1518	94	203	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.113	93	203	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.0458	98	203	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	78.0324	90	203	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.7339	96	203	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	77.7308	82	203	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.7164	88	203	95	below_threshold
Confluentibacter citreus	strain=XJNY	GCA_002807055.1	2007307	2007307	type	True	77.5822	82	203	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	77.413	67	203	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	77.2593	73	203	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	77.127	83	203	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.9846	75	203	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.9588	51	203	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.9414	67	203	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:56:23,703] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10736/tc_result.tsv
[2023-03-15 23:56:23,711] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:56:23,711] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:56:23,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d63e251-0fd7-4cb6-b0f3-c6f46ab6afdf/dqc_reference/checkm_data
[2023-03-15 23:56:23,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:56:23,717] [INFO] Task started: CheckM
[2023-03-15 23:56:23,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10736/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10736/checkm_input OceanDNA-b10736/checkm_result
[2023-03-15 23:56:45,280] [INFO] Task succeeded: CheckM
[2023-03-15 23:56:45,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:56:45,341] [INFO] ===== Completeness check finished =====
[2023-03-15 23:56:45,342] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:56:45,342] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10736/markers.fasta)
[2023-03-15 23:56:45,343] [INFO] Task started: Blastn
[2023-03-15 23:56:45,343] [INFO] Running command: blastn -query OceanDNA-b10736/markers.fasta -db /var/lib/cwl/stg1d63e251-0fd7-4cb6-b0f3-c6f46ab6afdf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10736/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:56:46,161] [INFO] Task succeeded: Blastn
[2023-03-15 23:56:46,165] [INFO] Selected 19 target genomes.
[2023-03-15 23:56:46,165] [INFO] Target genome list was writen to OceanDNA-b10736/target_genomes_gtdb.txt
[2023-03-15 23:56:46,340] [INFO] Task started: fastANI
[2023-03-15 23:56:46,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg006b4de1-26a0-4af8-ad71-ce9b3b95722b/OceanDNA-b10736.fa --refList OceanDNA-b10736/target_genomes_gtdb.txt --output OceanDNA-b10736/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:56:57,465] [INFO] Task succeeded: fastANI
[2023-03-15 23:56:57,476] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:56:57,476] [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_003425985.1	s__Mariniflexile sp002848895	79.8256	125	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017814435.1	s__Mariniflexile gromovii	79.7389	122	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	79.7334	127	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.9501	120	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	78.6852	91	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	78.3888	96	203	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_002843175.1	s__Confluentibacter flavum	78.3599	90	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.3476	91	203	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_000789235.1	s__Wocania ichthyoenteri	78.3112	106	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.113	93	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.0753	94	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	78.0368	90	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	77.8315	86	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	77.8082	96	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806995.1	s__Confluentibacter lentus	77.7308	82	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.7164	88	203	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_015355625.1	s__Tamlana_A sp015355625	77.3693	83	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006148925.1	s__Algibacter_D aestuarii	77.127	83	203	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_007997385.1	s__Seonamhaeicola algicola	76.9869	74	203	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:56:57,481] [INFO] GTDB search result was written to OceanDNA-b10736/result_gtdb.tsv
[2023-03-15 23:56:57,492] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:56:57,501] [INFO] DFAST_QC result json was written to OceanDNA-b10736/dqc_result.json
[2023-03-15 23:56:57,501] [INFO] DFAST_QC completed!
[2023-03-15 23:56:57,501] [INFO] Total running time: 0h0m55s