[2023-06-19 14:06:22,681] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:06:22,684] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:06:22,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg8026c392-bad1-4b8f-9c1e-a6ee9ff22e6e/dqc_reference
[2023-06-19 14:06:23,919] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:06:23,920] [INFO] Task started: Prodigal
[2023-06-19 14:06:23,920] [INFO] Running command: gunzip -c /var/lib/cwl/stg480c6ee2-63ec-4a96-88ea-b9d0baa8a1f1/GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:06:30,447] [INFO] Task succeeded: Prodigal
[2023-06-19 14:06:30,447] [INFO] Task started: HMMsearch
[2023-06-19 14:06:30,447] [INFO] Running command: hmmsearch --tblout GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8026c392-bad1-4b8f-9c1e-a6ee9ff22e6e/dqc_reference/reference_markers.hmm GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:06:30,650] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:06:30,652] [INFO] Found 6/6 markers.
[2023-06-19 14:06:30,677] [INFO] Query marker FASTA was written to GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 14:06:30,677] [INFO] Task started: Blastn
[2023-06-19 14:06:30,678] [INFO] Running command: blastn -query GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8026c392-bad1-4b8f-9c1e-a6ee9ff22e6e/dqc_reference/reference_markers.fasta -out GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:06:31,259] [INFO] Task succeeded: Blastn
[2023-06-19 14:06:31,264] [INFO] Selected 6 target genomes.
[2023-06-19 14:06:31,265] [INFO] Target genome list was writen to GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 14:06:31,266] [INFO] Task started: fastANI
[2023-06-19 14:06:31,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg480c6ee2-63ec-4a96-88ea-b9d0baa8a1f1/GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:06:35,713] [INFO] Task succeeded: fastANI
[2023-06-19 14:06:35,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8026c392-bad1-4b8f-9c1e-a6ee9ff22e6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:06:35,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8026c392-bad1-4b8f-9c1e-a6ee9ff22e6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:06:35,715] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:06:35,716] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 14:06:35,716] [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
--------------------------------------------------------------------------------
[2023-06-19 14:06:35,718] [INFO] DFAST Taxonomy check result was written to GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 14:06:35,718] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:06:35,718] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:06:35,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8026c392-bad1-4b8f-9c1e-a6ee9ff22e6e/dqc_reference/checkm_data
[2023-06-19 14:06:35,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:06:35,752] [INFO] Task started: CheckM
[2023-06-19 14:06:35,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 14:07:00,965] [INFO] Task succeeded: CheckM
[2023-06-19 14:07:00,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:07:00,991] [INFO] ===== Completeness check finished =====
[2023-06-19 14:07:00,991] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:07:00,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 14:07:00,992] [INFO] Task started: Blastn
[2023-06-19 14:07:00,992] [INFO] Running command: blastn -query GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8026c392-bad1-4b8f-9c1e-a6ee9ff22e6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:07:01,955] [INFO] Task succeeded: Blastn
[2023-06-19 14:07:01,963] [INFO] Selected 11 target genomes.
[2023-06-19 14:07:01,963] [INFO] Target genome list was writen to GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:07:01,964] [INFO] Task started: fastANI
[2023-06-19 14:07:01,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg480c6ee2-63ec-4a96-88ea-b9d0baa8a1f1/GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:07:08,458] [INFO] Task succeeded: fastANI
[2023-06-19 14:07:08,468] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:07:08,469] [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_016764995.1	s__Arctic96AD-7 sp016764995	99.1917	682	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012964265.1	s__Arctic96AD-7 sp012964265	83.8701	469	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.25	98.98	0.81	0.73	8	-
GCA_018645085.1	s__Arctic96AD-7 sp018645085	82.0705	579	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685535.1	s__Arctic96AD-7 sp002685535	81.35	534	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.44	95.94	0.78	0.68	5	-
GCA_014381795.1	s__Arctic96AD-7 sp014381795	81.1409	390	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002082305.1	s__Arctic96AD-7 sp002082305	79.7471	468	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	98.68	95.22	0.86	0.64	13	-
GCA_902513935.1	s__Arctic96AD-7 sp902513935	79.2514	209	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182865.1	s__Arctic96AD-7 sp905182865	79.1772	473	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.26	97.17	0.94	0.88	7	-
GCA_004213175.1	s__Arctic96AD-7 sp002704555	78.5773	332	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.39	96.63	0.73	0.69	4	-
GCA_014382365.1	s__Arctic96AD-7 sp014382365	77.8986	342	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.95	99.95	0.98	0.98	2	-
GCA_001627865.1	s__Arctic96AD-7 sp001627865	76.9562	250	852	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.71	99.45	0.95	0.94	9	-
--------------------------------------------------------------------------------
[2023-06-19 14:07:08,473] [INFO] GTDB search result was written to GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 14:07:08,474] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:07:08,479] [INFO] DFAST_QC result json was written to GCA_937889435.1_SRR5494785_bin.101_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 14:07:08,480] [INFO] DFAST_QC completed!
[2023-06-19 14:07:08,480] [INFO] Total running time: 0h0m46s