[2023-06-13 19:39:04,304] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:39:04,315] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:39:04,315] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3aa44fd-bb68-46c0-b55e-e611a1b49e1f/dqc_reference
[2023-06-13 19:39:05,980] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:39:05,981] [INFO] Task started: Prodigal
[2023-06-13 19:39:05,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ef36384-3dbc-4b68-8ea9-1f29217124d7/GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:39:11,212] [INFO] Task succeeded: Prodigal
[2023-06-13 19:39:11,213] [INFO] Task started: HMMsearch
[2023-06-13 19:39:11,213] [INFO] Running command: hmmsearch --tblout GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3aa44fd-bb68-46c0-b55e-e611a1b49e1f/dqc_reference/reference_markers.hmm GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:39:11,452] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:39:11,453] [INFO] Found 6/6 markers.
[2023-06-13 19:39:11,478] [INFO] Query marker FASTA was written to GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 19:39:11,478] [INFO] Task started: Blastn
[2023-06-13 19:39:11,478] [INFO] Running command: blastn -query GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3aa44fd-bb68-46c0-b55e-e611a1b49e1f/dqc_reference/reference_markers.fasta -out GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:39:12,068] [INFO] Task succeeded: Blastn
[2023-06-13 19:39:12,071] [INFO] Selected 24 target genomes.
[2023-06-13 19:39:12,071] [INFO] Target genome list was writen to GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 19:39:12,072] [INFO] Task started: fastANI
[2023-06-13 19:39:12,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ef36384-3dbc-4b68-8ea9-1f29217124d7/GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:39:26,277] [INFO] Task succeeded: fastANI
[2023-06-13 19:39:26,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3aa44fd-bb68-46c0-b55e-e611a1b49e1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:39:26,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3aa44fd-bb68-46c0-b55e-e611a1b49e1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:39:26,291] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:39:26,291] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 19:39:26,291] [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
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	79.5482	272	881	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	78.9061	105	881	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	78.8561	108	881	95	below_threshold
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	78.227	59	881	95	below_threshold
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	78.0936	113	881	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	77.6436	59	881	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	77.2295	75	881	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	77.2228	80	881	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	77.0565	52	881	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	76.7877	56	881	95	below_threshold
[Clostridium] fimetarium	strain=DSM 9179	GCA_900111235.1	99656	99656	type	True	76.2276	70	881	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 19:39:26,293] [INFO] DFAST Taxonomy check result was written to GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 19:39:26,293] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:39:26,293] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:39:26,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3aa44fd-bb68-46c0-b55e-e611a1b49e1f/dqc_reference/checkm_data
[2023-06-13 19:39:26,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:39:26,323] [INFO] Task started: CheckM
[2023-06-13 19:39:26,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 19:39:47,574] [INFO] Task succeeded: CheckM
[2023-06-13 19:39:47,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 19:39:47,614] [INFO] ===== Completeness check finished =====
[2023-06-13 19:39:47,614] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:39:47,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 19:39:47,615] [INFO] Task started: Blastn
[2023-06-13 19:39:47,615] [INFO] Running command: blastn -query GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3aa44fd-bb68-46c0-b55e-e611a1b49e1f/dqc_reference/reference_markers_gtdb.fasta -out GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:39:48,637] [INFO] Task succeeded: Blastn
[2023-06-13 19:39:48,642] [INFO] Selected 21 target genomes.
[2023-06-13 19:39:48,642] [INFO] Target genome list was writen to GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:39:48,646] [INFO] Task started: fastANI
[2023-06-13 19:39:48,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ef36384-3dbc-4b68-8ea9-1f29217124d7/GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:39:58,505] [INFO] Task succeeded: fastANI
[2023-06-13 19:39:58,518] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 19:39:58,518] [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_014287955.1	s__Lachnospira sp900316325	98.9408	781	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.86	98.35	0.93	0.88	10	conclusive
GCF_003458705.1	s__Lachnospira sp003537285	79.5358	250	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.4867	98.01	96.87	0.87	0.80	8	-
GCF_003464165.1	s__Lachnospira sp003451515	79.4705	238	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.95	97.44	0.88	0.84	9	-
GCA_900112995.1	s__Lachnospira rogosae_A	79.1621	281	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.05	98.51	0.91	0.85	17	-
GCA_900547255.1	s__Lachnospira sp900547255	78.8021	248	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.87	99.87	0.91	0.91	2	-
GCA_900772425.1	s__Lachnospira sp900772425	78.7292	131	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545725.1	s__Lachnospira sp900545725	78.6322	236	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.88	98.45	0.88	0.87	3	-
GCA_000436475.1	s__Lachnospira sp000436475	78.3433	231	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.97	97.42	0.90	0.86	10	-
GCA_000437735.1	s__Lachnospira sp000437735	78.318	193	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.81	98.12	0.91	0.82	10	-
GCA_900552795.1	s__Lachnospira sp900552795	78.2142	208	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.54	99.07	0.90	0.84	3	-
GCA_000436535.1	s__Lachnospira sp000436535	78.1467	228	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.91	98.77	0.95	0.93	6	-
GCA_002435585.1	s__Lachnospira sp002435585	78.1251	179	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017397445.1	s__Lachnospira sp017397445	77.9964	143	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394205.1	s__Lachnospira sp002394205	77.9052	145	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.96	99.94	0.94	0.91	3	-
GCF_018918265.1	s__Falcatimonas sp018918265	77.8283	128	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_017626275.1	s__Lachnospira sp017626275	77.7546	99	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587485.1	s__Lachnospira sp910587485	77.4818	143	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585095.1	s__Lachnospira sp910585095	77.3515	143	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551945.1	s__Lachnospira sp900551945	77.3186	184	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.31	99.16	0.89	0.87	3	-
GCA_902363805.1	s__Eubacterium_G sp000434315	76.8512	80	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
GCA_017935345.1	s__Coprococcus sp017935345	76.5303	55	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 19:39:58,520] [INFO] GTDB search result was written to GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 19:39:58,520] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:39:58,524] [INFO] DFAST_QC result json was written to GCA_938022015.1_SRR8114102_bin.8_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 19:39:58,524] [INFO] DFAST_QC completed!
[2023-06-13 19:39:58,524] [INFO] Total running time: 0h0m54s