[2023-06-29 12:25:22,103] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:25:22,105] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:25:22,105] [INFO] DQC Reference Directory: /var/lib/cwl/stgd65b1e17-eca2-45d4-8a95-419dff437716/dqc_reference
[2023-06-29 12:25:23,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:25:23,351] [INFO] Task started: Prodigal
[2023-06-29 12:25:23,351] [INFO] Running command: gunzip -c /var/lib/cwl/stg9872bd71-89f8-46d9-936c-3162caa32edc/GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:25:29,779] [INFO] Task succeeded: Prodigal
[2023-06-29 12:25:29,780] [INFO] Task started: HMMsearch
[2023-06-29 12:25:29,780] [INFO] Running command: hmmsearch --tblout GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd65b1e17-eca2-45d4-8a95-419dff437716/dqc_reference/reference_markers.hmm GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:25:30,026] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:25:30,028] [INFO] Found 6/6 markers.
[2023-06-29 12:25:30,053] [INFO] Query marker FASTA was written to GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 12:25:30,054] [INFO] Task started: Blastn
[2023-06-29 12:25:30,054] [INFO] Running command: blastn -query GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd65b1e17-eca2-45d4-8a95-419dff437716/dqc_reference/reference_markers.fasta -out GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:25:30,833] [INFO] Task succeeded: Blastn
[2023-06-29 12:25:30,837] [INFO] Selected 34 target genomes.
[2023-06-29 12:25:30,837] [INFO] Target genome list was writen to GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 12:25:30,839] [INFO] Task started: fastANI
[2023-06-29 12:25:30,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg9872bd71-89f8-46d9-936c-3162caa32edc/GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:25:50,128] [INFO] Task succeeded: fastANI
[2023-06-29 12:25:50,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd65b1e17-eca2-45d4-8a95-419dff437716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:25:50,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd65b1e17-eca2-45d4-8a95-419dff437716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:25:50,149] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:25:50,149] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:25:50,149] [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
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.9124	69	533	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.8732	66	533	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.845	68	533	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.7628	68	533	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.7246	109	533	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.6623	71	533	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	76.5103	59	533	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	76.4755	102	533	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	76.3505	54	533	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	76.3153	55	533	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.2488	77	533	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	76.0632	52	533	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.0208	59	533	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.9441	71	533	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.911	66	533	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	75.8793	72	533	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	75.8606	65	533	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	75.8296	77	533	95	below_threshold
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	75.8127	78	533	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.7627	54	533	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:25:50,151] [INFO] DFAST Taxonomy check result was written to GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 12:25:50,152] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:25:50,152] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:25:50,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd65b1e17-eca2-45d4-8a95-419dff437716/dqc_reference/checkm_data
[2023-06-29 12:25:50,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:25:50,186] [INFO] Task started: CheckM
[2023-06-29 12:25:50,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 12:26:15,093] [INFO] Task succeeded: CheckM
[2023-06-29 12:26:15,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:26:15,117] [INFO] ===== Completeness check finished =====
[2023-06-29 12:26:15,117] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:26:15,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 12:26:15,118] [INFO] Task started: Blastn
[2023-06-29 12:26:15,118] [INFO] Running command: blastn -query GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd65b1e17-eca2-45d4-8a95-419dff437716/dqc_reference/reference_markers_gtdb.fasta -out GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:26:16,481] [INFO] Task succeeded: Blastn
[2023-06-29 12:26:16,486] [INFO] Selected 12 target genomes.
[2023-06-29 12:26:16,486] [INFO] Target genome list was writen to GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:26:16,492] [INFO] Task started: fastANI
[2023-06-29 12:26:16,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg9872bd71-89f8-46d9-936c-3162caa32edc/GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:26:23,695] [INFO] Task succeeded: fastANI
[2023-06-29 12:26:23,713] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:26:23,714] [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
GCA_003989075.1	s__RXIX01 sp003989075	99.2922	498	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__RXIX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008933795.1	s__Contendobacter sp008933795	79.4537	258	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Contendobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391525.1	s__Competibacter_A sp002391525	79.1952	274	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter_A	95.0	99.79	99.79	0.93	0.93	2	-
GCA_003989065.1	s__RXIW01 sp003989065	79.1805	249	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__RXIW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699715.1	s__Competibacter sp016699715	78.7338	257	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003989085.1	s__RXIV01 sp003989085	78.6365	169	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__RXIV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012939995.1	s__Competibacter phosphatis	78.6087	252	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262135.1	s__Contendobacter sp018262135	78.5686	179	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Contendobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352185.1	s__Contendobacter sp002352185	78.2558	211	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Contendobacter	95.0	99.47	99.47	0.84	0.84	2	-
GCA_002433805.1	s__Competibacter_A sp002433805	78.166	167	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter_A	95.0	99.11	97.86	0.82	0.76	6	-
GCA_016713505.1	s__Competibacter_A sp016713505	77.967	206	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter_A	95.0	99.59	99.51	0.96	0.95	5	-
GCA_003527885.1	s__Competibacter_A sp003527885	77.7356	156	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:26:23,716] [INFO] GTDB search result was written to GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 12:26:23,717] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:26:23,722] [INFO] DFAST_QC result json was written to GCA_937862855.1_SRR5007354_bin.66_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 12:26:23,722] [INFO] DFAST_QC completed!
[2023-06-29 12:26:23,722] [INFO] Total running time: 0h1m2s